A simple, effective measure of synonymous codon usage bias, the Codon Adaptation Index, is detailed. The index uses a reference set of highly expressed genes from a species to assess the relative merits of each codon, and a score for a gene is calculated from the frequency of use of all codons in that gene. The index assesses the extent to which selection has been effective in moulding the pattern of codon usage. In that respect it is useful for predicting the level of expression of a gene, for assessing the adaptation of viral genes to their hosts, and for making comparisons of codon usage in different organisms. The index may also give an approximate indication of the likely success of heterologous gene expression.

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Comparison of plant mitochondrial (mt), chloroplast (cp) and nuclear (n) DNA sequences shows that the silent substitution rate in mtDNA is less than one-third that in cpDNA, which in turn evolves only half as fast as plant nDNA. The slower rate in mtDNA than in cpDNA is probably due to a lower mutation rate. Silent substitution rates in plant and mammalian mtDNAs differ by one or two orders of magnitude, whereas the rates in nDNAs may be similar. In cpDNA, the rate of substitution both at synonymous sites and in noncoding sequences in the inverted repeat is greatly reduced in comparison to single-copy sequences. The rate of cpDNA evolution appears to have slowed in some dicot lineages following the monocot/dicot split, and the slowdown is more conspicuous at nonsynonymous sites than at synonymous sites.Our current knowledge of the rates and mechanisms of molecular evolution has been derived largely from comparative studies of genes and proteins of animals (1, 2). Only recently has the study of the molecular biology of plants provided sufficient data to allow the evolution of plant genes to be investigated. Since the plant and animal kingdoms diverged about 1000 million years (Myr) ago, their patterns of evolution might have become very different. In fact, plants differ from animals in the organization oftheir organelle DNA by having a much larger and structurally more variable mitochondrial genome and by having a third (chloroplast) genome (3). So, do the rates of nucleotide substitution differ between animal and plant DNAs? Also, since in mammals mitochondrial DNA (mtDNA) evolves much faster than nuclear DNA (nDNA) (4), do the substitution rates vary greatly among the three plant genomes?Previous studies based on a few gene sequences or on restriction enzyme mapping have suggested that chloroplast genes have lower rates of nucleotide substitution than mammalian nuclear genes (3, 5) and that plant mtDNA evolves slowly in nucleotide sequence, though it undergoes frequent rearrangement (6). Restriction analysis (3, 7) has also suggested that the large inverted repeat (IR) sequences in chloroplast DNA (cpDNA) have lower rates of nucleotide substitution than the rest of the chloroplast genome. Available DNA sequence data from plants now allow a detailed investigation of the rates of nucleotide substitution in the three plant genomes, reconstruction of the phylogenetic relationships among some higher plants, and comparison of evolutionary rates among lineages.MATERIALS AND METHODS DNA sequences were taken from GenBank § and the literature; the sequences of liverwort and tobacco chloroplast genomes (8, 9) were kindly provided on disk by K. Ohyama and M. Sugiura.Numbers of nucleotide substitutions in noncoding sequences were calculated by the two-parameter method of Kimura (1); regions in which the correct alignment was not apparent were excluded from the analysis. Protein-coding genes were analyzed by the method of Li et al. (10) RESULTSRates of Evolution of the Three Plant Genomes. In Table 1 we compare the ...

The human AIDS viruses human immunodeficiency virus type 1 (HIV-1) and type 2 (HIV-2) represent cross-species (zoonotic) infections. Although the primate reservoir of HIV-2 has been clearly identified as the sooty mangabey (Cercocebus atys), the origin of HIV-1 remains uncertain. Viruses related to HIV-1 have been isolated from the common chimpanzee (Pan troglodytes), but only three such SIVcpz infections have been documented, one of which involved a virus so divergent that it might represent a different primate lentiviral lineage. In a search for the HIV-1 reservoir, we have now sequenced the genome of a new SIVcpzstrain (SIVcpzUS) and have determined, by mitochondrial DNA analysis, the subspecies identity of all known SIVcpz-infected chimpanzees. We find that two chimpanzee subspecies in Africa, the central P. t. troglodytes and the eastern P. t. schweinfurthii, harbour SIVcpz and that their respective viruses form two highly divergent (but subspecies-specific) phylogenetic lineages. All HIV-1 strains known to infect man, including HIV-1 groups M, N and O, are closely related to just one of these SIVcpz lineages, that found in P. t. troglodytes. Moreover, we find that HIV-1 group N is a mosaic of SIVcpzUS- and HIV-1-related sequences, indicating an ancestral recombination event in a chimpanzee host. These results, together with the observation that the natural range of P. t. troglodytes coincides uniquely with areas of HIV-1 group M, N and O endemicity, indicate that P. t. troglodytes is the primary reservoir for HIV-1 and has been the source of at least three independent introductions of SIVcpz into the human population.